Use super() now that we support only Python 3

However leave calls in cdef functions as is; 0-argument super() does not work in cdef or cpdef Cython functions (see cython/cython#3726). The explicit superclass calls in libctabixproxies.pyx were jumping straight to the grandparent class. Using `super()` instead uses NamedTupleProxy's versions of these methods, but it doesn't declare any so calls use the grandparent's methods unchanged. Update the calls in cdef functions similarly for explicitness. TODO TestVCFFromVariantFile similarly directly calls the grandparent's setUp()/tearDown() methods, but changes behaviour as it skips those of the direct parent. This deserves clarification.
pysam-developers · Nov 16, 2023 · c328702 · c328702
1 parent 33120e2
commit c328702
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Showing 6 changed files with 25 additions and 44 deletions.
diff --git a/linker_tests/link_pre_489/cy_build.py b/linker_tests/link_pre_489/cy_build.py
@@ -31,7 +31,7 @@ def is_pip_install():
 class CyExtension(Extension):
     def __init__(self, *args, **kwargs):
         self._init_func = kwargs.pop("init_func", None)
-        Extension.__init__(self, *args, **kwargs)
+        super().__init__(*args, **kwargs)
 
     def extend_includes(self, includes):
         self.include_dirs.extend(includes)
@@ -83,4 +83,4 @@ def build_extension(self, ext):
 
             ext.extra_link_args += ['-Wl,-rpath,$ORIGIN']
 
-        build_ext.build_extension(self, ext)
+        super().build_extension(ext)
diff --git a/pysam/libcalignmentfile.pyx b/pysam/libcalignmentfile.pyx
@@ -2076,8 +2076,7 @@ cdef class IteratorRowRegion(IteratorRow):
         if not samfile.has_index():
             raise ValueError("no index available for iteration")
 
-        IteratorRow.__init__(self, samfile,
-                             multiple_iterators=multiple_iterators)
+        super().__init__(samfile, multiple_iterators=multiple_iterators)
         with nogil:
             self.iter = sam_itr_queryi(
                 self.index,
@@ -2133,9 +2132,7 @@ cdef class IteratorRowHead(IteratorRow):
                  AlignmentFile samfile,
                  int n,
                  int multiple_iterators=False):
-
-        IteratorRow.__init__(self, samfile,
-                             multiple_iterators=multiple_iterators)
+        super().__init__(samfile, multiple_iterators=multiple_iterators)
 
         self.max_rows = n
         self.current_row = 0
@@ -2183,11 +2180,8 @@ cdef class IteratorRowAll(IteratorRow):
 
     """
 
-    def __init__(self, AlignmentFile samfile,
-                 int multiple_iterators=False):
-
-        IteratorRow.__init__(self, samfile,
-                             multiple_iterators=multiple_iterators)
+    def __init__(self, AlignmentFile samfile, int multiple_iterators=False):
+        super().__init__(samfile, multiple_iterators=multiple_iterators)
 
     def __iter__(self):
         return self
@@ -2226,11 +2220,8 @@ cdef class IteratorRowAllRefs(IteratorRow):
 
     """
 
-    def __init__(self, AlignmentFile samfile,
-                 multiple_iterators=False):
-
-        IteratorRow.__init__(self, samfile,
-                             multiple_iterators=multiple_iterators)
+    def __init__(self, AlignmentFile samfile, multiple_iterators=False):
+        super().__init__(samfile, multiple_iterators=multiple_iterators)
 
         if not samfile.has_index():
             raise ValueError("no index available for fetch")
@@ -2291,8 +2282,7 @@ cdef class IteratorRowSelection(IteratorRow):
     """
 
     def __init__(self, AlignmentFile samfile, positions, int multiple_iterators=True):
-
-        IteratorRow.__init__(self, samfile, multiple_iterators=multiple_iterators)
+        super().__init__(samfile, multiple_iterators=multiple_iterators)
 
         self.positions = positions
         self.current_pos = 0

diff --git a/pysam/libctabix.pyx b/pysam/libctabix.pyx
@@ -697,10 +697,8 @@ cdef class TabixIteratorParsed(TabixIterator):
     Returns parsed data.
     """
 
-    def __init__(self, 
-                 Parser parser):
-
-        TabixIterator.__init__(self)
+    def __init__(self, Parser parser):
+        super().__init__()
         self.parser = parser
 
     def __next__(self): 

diff --git a/pysam/libctabixproxies.pyx b/pysam/libctabixproxies.pyx
@@ -494,7 +494,7 @@ cdef class GTFProxy(NamedTupleProxy):
                  toDot(self.frame),
                  self.attributes))
         else: 
-            return TupleProxy.__str__(self)
+            return super().__str__()
 
     def invert(self, int lcontig):
         '''invert coordinates to negative strand coordinates
@@ -732,7 +732,7 @@ cdef class BedProxy(NamedTupleProxy):
 
         nbytes does not include the terminal '\0'.
         '''
-        TupleProxy.update(self, buffer, nbytes)
+        NamedTupleProxy.update(self, buffer, nbytes)
 
         if self.nfields < 3:
             raise ValueError(
@@ -754,11 +754,10 @@ cdef class BedProxy(NamedTupleProxy):
     #    def __get__( self ): return self.end
 
     def __str__(self):
-
         cdef int save_fields = self.nfields
         # ensure fields to use correct format
         self.nfields = self.bedfields
-        retval = TupleProxy.__str__(self)
+        retval = super().__str__()
         self.nfields = save_fields
         return retval
 
@@ -801,7 +800,7 @@ cdef class VCFProxy(NamedTupleProxy):
         
         nbytes does not include the terminal '\0'.
         '''
-        TupleProxy.update(self, buffer, nbytes)
+        NamedTupleProxy.update(self, buffer, nbytes)
 
         self.contig = self.fields[0]
         # vcf counts from 1 - correct here

diff --git a/setup.py b/setup.py
@@ -228,7 +228,7 @@ class cythonize_sdist(sdist):
     def run(self):
         from Cython.Build import cythonize
         cythonize(self.distribution.ext_modules)
-        sdist.run(self)
+        super().run()
 
 
 # Override Cythonised build_ext command to customise macOS shared libraries.
@@ -237,7 +237,7 @@ class CyExtension(Extension):
     def __init__(self, *args, **kwargs):
         self._init_func = kwargs.pop("init_func", None)
         self._prebuild_func = kwargs.pop("prebuild_func", None)
-        Extension.__init__(self, *args, **kwargs)
+        super().__init__(*args, **kwargs)
 
     def extend_includes(self, includes):
         self.include_dirs.extend(includes)
@@ -274,7 +274,7 @@ def run(self):
             ldshared = os.environ.get('LDSHARED', sysconfig.get_config_var('LDSHARED'))
             os.environ['LDSHARED'] = ldshared.replace('-bundle', '')
 
-        build_ext.run(self)
+        super().run()
         try:
             if HTSLIB_MODE != 'separate':
                 self.check_ext_symbol_conflicts()
@@ -318,7 +318,7 @@ def build_extension(self, ext):
         if isinstance(ext, CyExtension) and ext._prebuild_func:
             ext._prebuild_func(ext, self.force)
 
-        build_ext.build_extension(self, ext)
+        super().build_extension(ext)
 
 
 class clean_ext(Command):

diff --git a/tests/tabix_test.py b/tests/tabix_test.py
@@ -230,8 +230,7 @@ class TestGZFile(IterationTest):
     with_comments = True
 
     def setUp(self):
-
-        IterationTest.setUp(self)
+        super().setUp()
         self.gzfile = pysam.GZIterator(self.filename)
 
     def testAll(self):
@@ -249,7 +248,7 @@ class TestIterationWithoutComments(IterationTest):
                             "example.gtf.gz")
 
     def setUp(self):
-        IterationTest.setUp(self)
+        super().setUp()
         self.tabix = pysam.TabixFile(self.filename)
 
     def tearDown(self):
@@ -374,9 +373,6 @@ class TestIterationWithComments(TestIterationWithoutComments):
 
     filename = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
 
-    def setUp(self):
-        TestIterationWithoutComments.setUp(self)
-
 
 class TestIterators(unittest.TestCase):
     filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
@@ -592,15 +588,14 @@ class TestVCFFromTabix(TestVCF):
                "filter", "info", "format")
 
     def setUp(self):
-
-        TestVCF.setUp(self)
+        super().setUp()
 
         self.tabix = pysam.TabixFile(self.tmpfilename + ".gz")
         self.compare = load_and_convert(self.filename)
 
     def tearDown(self):
         self.tabix.close()
-        TestVCF.tearDown(self)
+        super().tearDown()
 
     def testRead(self):
 
@@ -701,14 +696,13 @@ class TestVCFFromVCF(TestVCF):
     missing_quality = -1
 
     def setUp(self):
-
-        TestVCF.setUp(self)
+        super().setUp()
 
         self.vcf = pysam.VCF()
         self.compare = load_and_convert(self.filename, encode=False)
 
     def tearDown(self):
-        TestVCF.tearDown(self)
+        super().tearDown()
         self.vcf.close()
 
     def open_vcf(self, fn):